Ligand and Target Discovery by Fragment-Based Screening in Human Cells.

Advances in the synthesis and screening of small-molecule libraries have accelerated the discovery of chemical probes for studying biological processes. Still, only a small fraction of the human proteome has chemical ligands. Here, we describe a platform that marries fragment-based ligand discovery with quantitative chemical proteomics to map thousands of reversible small molecule-protein interactions directly in human cells, many of which can be site-specifically determined. We show that fragment hits can be advanced to furnish selective ligands that affect the activity of proteins heretofore lacking chemical probes. We further combine fragment-based chemical proteomics with phenotypic screening to identify small molecules that promote adipocyte differentiation by engaging the poorly characterized membrane protein PGRMC2. Fragment-based screening in human cells thus provides an extensive proteome-wide map of protein ligandability and facilitates the coordinated discovery of bioactive small molecules and their molecular targets.

A case of coexistent poorly differentiated adenosquamous carcinoma (glassy cell carcinoma), usual-type adenocarcinoma, and squamous cell carcinoma in situ of the cervix.

Poorly differentiated adenosquamous carcinoma (glassy cell carcinoma) of the cervix is extremely rare, accounting for 1-2% of all cervical cancers. Herein, we report a case with coexistent poorly differentiated adenosquamous carcinoma (glassy cell carcinoma), "usual-type" adenocarcinoma, and squamous cell carcinoma in situ of the cervix. A female patient in her 60 s was referred to our hospital and diagnosed with poorly differentiated adenosquamous carcinoma based on cervical cytology and biopsy. The tumor was classified as clinical stage IB1 cervical cancer following magnetic resonance imaging; radical hysterectomy was performed. Histopathological examination revealed poorly differentiated adenosquamous carcinoma (glassy cell carcinoma), usual-type adenocarcinoma, and squamous cell carcinoma in situ, all coexisting. All carcinoma regions showed identical sizes to high-risk human papillomavirus (HPV) in fragment analysis. The patient is currently alive, without evidence of recurrence, 31 months post surgery. In this case, three different carcinomas coexisted. Fragment analysis of the patient's HPV status suggested that all carcinomas were related to an infection with the same high-risk HPV type. To determine the precise mechanism of tumor development, i.e., whether the tumors were of the mixed or collision type, further studies are needed, including clonal analysis for the loss of heterozygosity pattern.

Alleviation of hand-skin roughness after use of alcohol-based hand rub with inhibitory effects on Staphylococcus aureus-producing δ-toxin.

INTRODUCTION: Staphylococcus aureus colonizes rough regions of the skin of the hand. Healing of S. aureus-mediated wounds is promoted by the application of RNA III inhibiting peptide, which inhibits the production of S. aureus virulence factors, including δ-toxin. Herein, we investigated the level of hand-skin roughness in healthcare professionals after they used an alcohol-based hand rub containing polyoxyethylene lauryl ether (formulation E), which inhibits S. aureus δ-toxin production. METHODS: The inhibition rate of S. aureus δ-toxin production by hand rubs, including formulation E, was calculated by quantifying S. aureus δ-toxin concentration in culture medium using high-performance liquid chromatography. Healthcare professionals used formulations E or S (reference alcohol-based hand rub) for 4 weeks. The surface evaluation of the scaliness (SEsc) value was used as an indicator of hand skin roughness. The ΔSEsc value was calculated by subtracting the SEsc value before using the alcohol-based hand rub from the SEsc value 4 weeks after use. RESULTS: The inhibition rates of S. aureus δ-toxin production by formulations E and S were 43% and 10%, respectively. Formulation E significantly reduced ΔSEsc. The difference in ΔSEsc values after using formulations E and S was significant. CONCLUSIONS: The inhibitory effect on S. aureus δ-toxin production was higher with formulation E than with formulation S. Compared to formulations S, formulation E was effective at reducing scaliness and alleviating hand-skin roughness. Furthermore, the inhibitory effect of formulation E on S. aureus δ-toxin production could be associated with a reduction in scaliness and alleviation of hand-skin roughness.

Plasma Heme Oxygenase-1 Levels and Carotid Atherosclerosis.

Background and Purpose- Heme oxygenase-1 (HO-1) catalyzes the oxidation of heme to generate carbon monoxide, biliverdin, and iron. Because these products have antiatherogenic properties, HO-1 may play a protective role against atherosclerosis. However, plasma HO-1 levels in patients with carotid atherosclerosis have not been reported. Methods- We investigated plasma HO-1 levels by ELISA in 136 subjects (age, 66±9 years) undergoing carotid ultrasonography. Results- Of the 136 study subjects, carotid plaque was found in 61 subjects (45%). Compared with 75 subjects without plaque, 61 with plaque were older and predominantly male ( P<0.05). Plasma HO-1 levels were higher in subjects with plaque than in those without plaque (median, 0.56 versus 0.44 ng/mL; P<0.05). The percentage of subjects with HO-1 level >0.50 ng/mL was higher in subjects with plaque than without plaque (66% versus 44%; P<0.025). In multivariate analysis, HO-1 level was a significant factor for carotid plaque independent of atherosclerotic risk factors. Odds ratio for plaque was 2.33 (95% CI, 1.15-4.75) for HO-1 level >0.50 ng/mL. Conclusions- Plasma HO-1 levels were high in subjects with carotid plaques, probably reflecting a protective response against carotid atherosclerosis.

Most Strange Dibaryon from Lattice QCD.

The ΩΩ system in the ^{1}S_{0} channel (the most strange dibaryon) is studied on the basis of the (2+1)-flavor lattice QCD simulations with a large volume (8.1 fm)^{3} and nearly physical pion mass m_{π}≃146 MeV at a lattice spacing of a≃0.0846 fm. We show that lattice QCD data analysis by the HAL QCD method leads to the scattering length a_{0}=4.6(6)(_{-0.5}^{+1.2}) fm, the effective range r_{eff}=1.27(3)(_{-0.03}^{+0.06}) fm, and the binding energy B_{ΩΩ}=1.6(6)(_{-0.6}^{+0.7}) MeV. These results indicate that the ΩΩ system has an overall attraction and is located near the unitary regime. Such a system can be best searched experimentally by the pair-momentum correlation in relativistic heavy-ion collisions.

Fate of the Tetraquark Candidate Z_{c}(3900) from Lattice QCD.

The possible exotic meson Z_{c}(3900), found in e^{+}e^{-} reactions, is studied by the method of coupled-channel scattering in lattice QCD. The interactions among πJ/ψ, ρη_{c}, and D[over ¯]D^{*} channels are derived from (2+1)-flavor QCD simulations at m_{π}=410-700 MeV. The interactions are dominated by the off-diagonal πJ/ψ-D[over ¯]D^{*} and ρη_{c}-D[over ¯]D^{*} couplings, which indicates that the Z_{c}(3900) is not a usual resonance but a threshold cusp. Semiphenomenological analyses with the coupled-channel interaction are also presented to confirm this conclusion.

Installing extra bicarbonate transporters in the cyanobacterium Synechocystis sp. PCC6803 enhances biomass production.

As a means to improve carbon uptake in the cyanobacterium Synechocystis sp. strain PCC6803, we engineered strains to contain additional inducible copies of the endogenous bicarbonate transporter BicA, an essential component of the CO2-concentrating mechanism in cyanobacteria. When cultured under atmospheric CO2 pressure, the strain expressing extra BicA transporters (BicA(+) strain) grew almost twice as fast and accumulated almost twice as much biomass as the control strain. When enriched with 0.5% or 5% CO2, the BicA(+) strain grew slower than the control but still showed a superior biomass production. Introducing a point mutation in the large C-terminal cytosolic domain of the inserted BicA, at a site implicated in allosteric regulation of transport activity, resulted in a strain (BicA(+)(T485G) strain) that exhibited pronounced cell aggregation and failed to grow at 5% CO2. However, the bicarbonate uptake capacity of the induced BicA(+)(T485G) was twice higher than for the wild-type strain. Metabolic analyses, including phenotyping by synchrotron-radiation Fourier transform Infrared spectromicroscopy, scanning electron microscopy, and lectin staining, suggest that the excess assimilated carbon in BicA(+) and BicA(+)(T485G) cells was directed into production of saccharide-rich exopolymeric substances. We propose that the increased capacity for CO2 uptake in the BicA(+) strain can be capitalized on by re-directing carbon flux from exopolymeric substances to other end products such as fuels or high-value chemicals.

[Induction chemotherapy with S-1/oxaliplatin prevented colostomy in a patient with advanced rectal cancer].

A 72-year-old woman was admitted to our hospital with bloody stools and constipation. She was diagnosed with advanced lower rectal cancer with multiple liver and pulmonary metastases. Because the rectal cancer was located 2 cm from the anal verge, we suggested she undergo an abdominoperineal resection(Miles operation), but she refused to undergo a colostomy. Then, 6 courses of chemotherapy with S-1/oxaliplatin(SOX)were administered, and the local tumor, liver metastases, and pulmonary metastases were all significantly decreased in size(reduction rate 60%). After chemotherapy, she chose to undergo low anterior resection(LAR), D2. Postoperative recovery was uneventful, and she currently has stable disease with adjuvant SOX chemotherapy. Induction SOX chemotherapy was considered to be useful for maintaining the quality of life(QOL) in a patient with advanced rectal cancer.

Identification and structure determination of novel anti-inflammatory mediator resolvin E3, 17,18-dihydroxyeicosapentaenoic acid.

Bioactive mediators derived from omega-3 eicosapentaenoic acid (EPA) elicit potent anti-inflammatory actions. Here, we identified novel EPA metabolites, including 8,18-dihydroxyeicosapentaenoic acid (8,18-diHEPE), 11,18-diHEPE, 12,18-diHEPE, and 17,18-diHEPE from 18-HEPE. Unlike resolvins E1 and E2, both of which are biosynthesized by neutrophils via the 5-lipoxygenase pathway, these metabolites are biosynthesized by eosinophils via the 12/15-lipoxygenase pathway. Among them, two stereoisomers of 17,18-diHEPE, collectively termed resolvin E3 (RvE3), displayed a potent anti-inflammatory action by limiting neutrophil infiltration in zymosan-induced peritonitis. The planar structure of RvE3 was unambiguously determined to be 17,18-dihydroxy-5Z,8Z,11Z,13E,15E-EPE by high resolution NMR, and the two stereoisomers were assigned to have 17,18R- and 17,18S-dihydroxy groups, respectively, using chemically synthesized 18R- and 18S-HEPE as precursors. Both 18R- and 18S-RvE3 inhibited neutrophil chemotaxis in vitro at low nanomolar concentrations. These findings suggest that RvE3 contributes to the beneficial actions of EPA in controlling inflammation and related diseases.

Equation of state for nucleonic matter and its quark mass dependence from the nuclear force in lattice QCD.

Quark mass dependence of the equation of state (EOS) for nucleonic matter is investigated, on the basis of the Brueckner-Hartree-Fock method with the nucleon-nucleon interaction extracted from lattice QCD simulations. We observe saturation of nuclear matter at the lightest available quark mass corresponding to the pseudoscalar meson mass ≃469 MeV. Mass-radius relation of the neutron stars is also studied with the EOS for neutron-star matter from the same nuclear force in lattice QCD. We observe that the EOS becomes stiffer and thus the maximum mass of neutron star increases as the quark mass decreases toward the physical point.

Synthesis and antimalarial activity of calothrixins A and B, and their N-alkyl derivatives.

We synthesized calothrixin B using our developed biomimetic method and derived N-alkyl-calothrixins A and B. The in vitro antimalarial activity of the calothrixin derivatives, including calothrixins A and B, against the Plasmodium falciparum FCR-3 strain was evaluated. All test compounds exhibited antimalarial activity over a concentration range of 6.4×10(-6)-1.2×10(-7) M.

A New Compartment Model of COVID-19 Transmission: The Broken-Link Model.

We propose a new compartment model of COVID-19 spread, the broken-link model, which includes the effect from unconnected infectious links of the transmission. The traditional SIR-type epidemic models are widely used to analyze the spread status, and the models show the exponential growth of the number of infected people. However, even in the early stage of the spread, it is proven by the actual data that the exponential growth did not occur all over the world. We presume this is caused by the suppression of secondary and higher-order transmissions of COVID-19. We find that the proposed broken-link model quantitatively describes the mechanism of this suppression, which leads to the shape of epicurves of confirmed cases are governed by the probability of unconnected infectious links, and the magnitudes of the cases are proportional to expR0 in each infectious surge generated by a virus of the basic reproduction number R0, and is consistent with the actual data.

A Collaborative Study on the Classification of Silicone Oil Droplets and Protein Particles Using Flow Imaging Method.

In this study, we conducted a collaborative study on the classification between silicone oil droplets and protein particles detected using the flow imaging (FI) method toward proposing a standardized classifier/model. We compared four approaches, including a classification filter composed of particle characteristic parameters, principal component analysis, decision tree, and convolutional neural network in the performance of the developed classifier/model. Finally, the points to be considered were summarized for measurement using the FI method, and for establishing the classifier/model using machine learning to differentiate silicone oil droplets and protein particles.

Bound H dibaryon in flavor SU(3) limit of lattice QCD.

The flavor-singlet H dibaryon, which has strangeness -2 and baryon number 2, is studied by the approach recently developed for the baryon-baryon interactions in lattice QCD. The flavor-singlet central potential is derived from the spatial and imaginary-time dependence of the Nambu-Bethe-Salpeter wave function measured in N(f)=3 full QCD simulations with the lattice size of L≃2,3,4 fm. The potential is found to be insensitive to the volume, and it leads to a bound H dibaryon with the binding energy of 30-40 MeV for the pseudoscalar meson mass of 673-1015 MeV.

Predicting solvent stability in aprotic electrolyte Li-air batteries: nucleophilic substitution by the superoxide anion radical (O2(•-)).

There is increasing evidence that cyclic and linear carbonates, commonly used solvents in Li ion battery electrolytes, are unstable in the presence of superoxide and thus are not suitable for use in rechargeable Li-air batteries employing aprotic electrolytes. A detailed understanding of related decomposition mechanisms provides an important basis for the selection and design of stable electrolyte materials. In this article, we use density functional theory calculations with a Poisson-Boltzmann continuum solvent model to investigate the reactivity of several classes of aprotic solvents in nucleophilic substitution reactions with superoxide. We find that nucleophilic attack by O(2)(•-) at the O-alkyl carbon is a common mechanism of decomposition of organic carbonates, sulfonates, aliphatic carboxylic esters, lactones, phosphinates, phosphonates, phosphates, and sulfones. In contrast, nucleophilic reactions of O(2)(•-) with phenol esters of carboxylic acids and O-alkyl fluorinated aliphatic lactones proceed via attack at the carbonyl carbon. Chemical functionalities stable against nucleophilic substitution by superoxide include N-alkyl substituted amides, lactams, nitriles, and ethers. The results establish that solvent reactivity is strongly related to the basicity of the organic anion displaced in the reaction with superoxide. Theoretical calculations are complemented by cyclic voltammetry to study the electrochemical reversibility of the O(2)/O(2)(•-) couple containing tetrabutylammonium salt and GCMS measurements to monitor solvent stability in the presence of KO(2)(•) and a Li salt. These experimental methods provide efficient means for qualitatively screening solvent stability in Li-air batteries. A clear correlation between the computational and experimental results is established. The combination of theoretical and experimental techniques provides a powerful means for identifying and designing stable solvents for rechargeable Li-air batteries.

Heterologous expression of Aspergillus oryzae xylose reductase and xylitol dehydrogenase genes facilitated xylose utilization in the yeast Saccharomyces cerevisiae.

The cDNA encoding a putative xylose reductase (xyrA) from Aspergillus oryzae was cloned and coexpressed in the yeast Saccharomyces cerevisiae with A. oryzae xylitol dehydrogenase cDNA (xdhA). XyrA exhibited NADPH-dependent xylose reductase activity. The S. cerevisiae strain, overexpressing the xyrA, xdhA, endogenous XKS1, and TAL1 genes, grew on xylose as sole carbon source, and produced ethanol.

Extraction of hadron interactions above inelastic threshold in lattice QCD.

We propose a new method to extract hadron interactions above inelastic threshold from the Nambu-Bethe-Salpeter amplitude in lattice QCD. We consider the scattering such as A + B → C + D, where A, B, C, D are names of different 1-particle states. An extension to cases where particle productions occur during scatterings is also discussed.

Photometric Screening of Tetrabromobisphenol A in Resin Using Iron(III) Nitrate/Hexacyanoferrate(III) Mixture as a Colorimetric Reagent.

This study aims to provide a simple way to identify the possibility of tetrabromobisphenol A (TBBPA) present in polymers without the need for complicated separation with expensive equipment. Since the presence of phenolic hydroxyl groups is known to be identifiable by the reduction of Fe3+ to Fe2+ in a ferric coloring reagent, the possibility of TBBPA being present in a polymer can be screened by a photometric measurement. A mixed solution of iron(III) nitrate and potassium hexacyanide(III) acid was used as a ferric coloring reagent. With this method, the concentration of TBBPA can be estimated from the photometric absorbance corresponding to the depth of the blue color produced by reduction of the ferric reagent in the presence of Fe(NO3)3. The limit of detection (LOD) was determined to be approximately 2 mg/kg using the Student's t-test (99% confidence), and a reproducibility of approximately 3% was determined by the relative standard deviation (RSD) from measurements of calibration samples (n = 7). Furthermore, TBBPA in actual polymer samples was screened without the need for any complex processing steps. Because this colorimetric method measures TBBPA by detecting phenolic groups, it may overestimate the TBBPA concentration in the presence of other similar phenolic substances. Nonetheless, this simple colorimetric method should help to quickly identify the presence of TBBPA in various polymers.

Comparison of In Vivo Transportability of Anti-Methicillin-Resistant Staphylococcus aureus (MRSA) Agents Into Intracellular and Extracellular Tissue Spaces in Rats.

The pathogenic bacterium Staphylococcus aureus can penetrate host cells. However, intracellular S. aureus is not considered during antimicrobial agent selection in clinical chemotherapy because of the lack of information about drug transportability into cells in vivo. We focused on agents used to treat methicillin-resistant S. aureus (MRSA) (vancomycin, arbekacin, linezolid, and daptomycin) and indirectly assessed the drug levels in intracellular compartment using plasma, tissue homogenates, and interstitial fluid (ISF) samples from the skin of rats using the microneedle array technique. Lower drug levels were observed in the ISF than in the plasma for daptomycin but extracellular and intracellular drug levels were comparable. In contrast, vancomycin, arbekacin, and linezolid showed higher concentrations in the ISF than in the plasma. Intracellular transport was estimated only for arbekacin. Stasis of vancomycin in the ISF was also observed. These results suggest that both low vancomycin exposure against intracellular S. aureus infection and long-term subinhibitory drug levels in the ISF contribute to the failure of treatment and emergence of antibiotic resistance. Based on its pharmacokinetic characteristics in niche extravascular tissue spaces, arbekacin may be suitable for achieving sufficient clinical outcomes for MRSA infection because the drug is widely distributed in extracellular and intracellular compartments.